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Abduch NG, Reolon HG, Ligori VA, Silva RMDO, Veríssimo CJ, Paz CCP, Stafuzza NB. Resistance to natural tick infestation varies with age and coat and hair traits in a tropically adapted beef cattle breed. Vet Parasitol Reg Stud Reports 2024; 50:101017. [PMID: 38644040 DOI: 10.1016/j.vprsr.2024.101017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/23/2024]
Abstract
Rhipicephalus (Boophilus) microplus causes considerable livestock production losses. Knowledge of the traits that influence tick resistance contributes to the development of breeding strategies designed to improve herd productivity. Within this context, this study evaluated the resistance of Caracu, a tropically adapted cattle breed, to R. microplus. Tick count, hair length, coat thickness, and coat color were evaluated in 202 naturally tick-infested females (cows and heifers) over a period of 18 months. Blood samples were collected from all animals during the winter season for hematological analysis. Data were analyzed using Pearson correlations, generalized linear models, and principal component analysis. Correlation coefficients of tick count with coat color, coat thickness, and hair length were estimated within each season. Hematological parameters were only included in the winter season analysis and were analyzed by the restricted maximum likelihood method using log-transformed data. No differences in blood parameters were observed between animals with and without ticks. However, tick count was negatively correlated with erythrocytes (-0.29) and hematocrit (-0.24) and positively correlated with mean corpuscular hemoglobin (0.21) and mean corpuscular hemoglobin concentration (0.25). These findings suggest that higher tick counts lead to a decrease in erythrocytes but also to an increase in the amount of hemoglobin per erythrocyte, which could reduce the damage caused by low erythrocyte levels due to tick hematophagy, delaying or preventing anemia. Although tick infestation on pasture was demonstrated by the infestation of all staff members during herd management, none of the animals exhibited high tick counts, providing evidence of resistance of Caracu animals to R. microplus. Tick infestation was influenced by age class (cows > heifers), season (spring and summer > fall and winter), coat thickness (>1.5 mm > <1.5 mm), and hair length (>6 mm > <6 mm). Three components were extracted by principal component analysis, which accounted for 69.46% of data variance. The findings of this study will contribute to the development of efficient strategies aimed at reducing economic losses due to tick infestation and could be applied in animal breeding to select for tick resistance traits, reducing chemical control strategies and consequently improving sustainable livestock production.
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Affiliation(s)
- Natalya Gardezani Abduch
- Department of Genetics, Ribeirao Preto Medical School (FMRP), University of Sao Paulo (USP), Ribeirao Preto, SP 140349-900, Brazil.
| | | | - Viviane Andrade Ligori
- Beef Cattle Research Center, Animal Science Institute (IZ), Sertaozinho, SP 14160-900, Brazil.
| | | | - Cecília José Veríssimo
- Sao Paulo Agency of Agribusiness and Technology, Animal Science Institute (IZ), Nova Odessa, SP 13380-011, Brazil.
| | - Claudia Cristina Paro Paz
- Department of Genetics, Ribeirao Preto Medical School (FMRP), University of Sao Paulo (USP), Ribeirao Preto, SP 140349-900, Brazil; Sustainable Livestock Research Center, Animal Science Institute, Sao Jose do Rio Preto, SP 15130-000, Brazil
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Freitas LA, Savegnago RP, Alves AAC, Stafuzza NB, Pedrosa VB, Rocha RA, Rosa GJM, Paz CCP. Genome-enabled prediction of indicator traits of resistance to gastrointestinal nematodes in sheep using parametric models and artificial neural networks. Res Vet Sci 2024; 166:105099. [PMID: 38091815 DOI: 10.1016/j.rvsc.2023.105099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 11/15/2023] [Accepted: 11/19/2023] [Indexed: 01/01/2024]
Abstract
This study aimed to assess the predictive ability of parametric models and artificial neural network method for genomic prediction of the following indicator traits of resistance to gastrointestinal nematodes in Santa Inês sheep: packed cell volume (PCV), fecal egg count (FEC), and Famacha© method (FAM). After quality control, the number of genotyped animals was 551 (PCV), 548 (FEC), and 565 (FAM), and 41,676 SNP. The average prediction accuracy (ACC) calculated by Pearson correlation between observed and predicted values and mean squared errors (MSE) were obtained using genomic best unbiased linear predictor (GBLUP), BayesA, BayesB, Bayesian least absolute shrinkage and selection operator (BLASSO), and Bayesian regularized artificial neural network (three and four hidden neurons, BRANN_3 and BRANN_4, respectively) in a 5-fold cross-validation technique. The average ACC varied from moderate to high according to the trait and models, ranging between 0.418 and 0.546 (PCV), between 0.646 and 0.793 (FEC), and between 0.414 and 0.519 (FAM). Parametric models presented nearly the same ACC and MSE for the studied traits and provided better accuracies than BRANN. The GBLUP, BayesA, BayesB and BLASSO models provided better accuracies than the BRANN_3 method, increasing by around 23% for PCV, and 18.5% for FEC. In conclusion, parametric models are suitable for genome-enabled prediction of indicator traits of resistance to gastrointestinal nematodes in sheep. Due to the small differences in accuracy found between them, the use of the GBLUP model is recommended due to its lower computational costs.
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Affiliation(s)
- L A Freitas
- University of Sao Paulo, Department of Genetics, Ribeirão Preto, São Paulo 14049-900, Brazil; University of Wisconsin, Department of Animal and Dairy Sciences, Madison 53706, USA.
| | - R P Savegnago
- Michigan State University, Department of Animal Science, MI 48864, USA.
| | - A A C Alves
- University of Wisconsin, Department of Animal and Dairy Sciences, Madison 53706, USA.
| | - N B Stafuzza
- Sustainable Livestock Research Center, Animal Science Institute, São José do Rio Preto, São Paulo 15130-000, Brazil
| | - V B Pedrosa
- State University of Ponta Grossa, Ponta Grossa, Paraná 84030-900, Brazil.
| | - R A Rocha
- State University of Ponta Grossa, Ponta Grossa, Paraná 84030-900, Brazil.
| | - G J M Rosa
- University of Wisconsin, Department of Animal and Dairy Sciences, Madison 53706, USA.
| | - C C P Paz
- University of Sao Paulo, Department of Genetics, Ribeirão Preto, São Paulo 14049-900, Brazil; Sustainable Livestock Research Center, Animal Science Institute, São José do Rio Preto, São Paulo 15130-000, Brazil.
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Stafuzza NB, Freitas ACD, Mioto MB, Silva RMDO, Fragomeni BDO, Pedrosa VB, Costa RLDD, Paz CCPD. Weighted single-step genome-wide association study and functional enrichment analyses for gastrointestinal nematode resistance traits in Santa Ines sheep. Vet Parasitol 2023; 323:110047. [PMID: 37857178 DOI: 10.1016/j.vetpar.2023.110047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 10/21/2023]
Abstract
This study aimed to identify genomic regions, pathways, and putative candidate genes associated with resistance to gastrointestinal nematode in Santa Ines sheep. The phenotypic information comprised 5529 records from 1703 naturally infected animals. After genomic data quality control, 37,511 SNPs from 589 animals were available. The weighted single-step approach for genome-wide association study was performed to estimate the SNP effects and variances accounted by 10-SNP sliding windows. Confirming the polygenic nature of the studied traits, 20, 22, 21, and 19 genomic windows that explained more than 0.5% of the additive genetic variance were identified for fecal egg counts (FEC), Famacha© (FAM), packed cell volume (PCV), and total plasma protein (TPP), respectively. A total of 81, 122, 106, and 101 protein-coding genes were found in windows associated with FEC, FAM, PCV, and TPP, respectively. Several protein-coding genes related to the immune system and inflammatory response functions were identified within those genomic regions, such as ADCY9, ADRB2, BRAF, CADM1, CCL20, CD70, CREBBP, FNBP1, HTR4, IL16, IL22, IL26, MAPK8, NDFIP1, NLRC3, PAK5, PLCB1, PLCB4, ROCK1, TEK, TNFRSF12A, and VAV1. Functional enrichment analysis by DAVID tool also revealed many significant (P < 0.05) pathways and Gene Ontology terms that could be related to resistance to gastrointestinal nematode in Santa Ines sheep, such as chemokine signaling pathway (oas04062), cAMP signaling pathway (oas04024), cGMP-PKG signaling pathway (Oas04022), platelet activation (Oas04611), Rap1 signaling pathway (oas04015), and oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705). These results contribute to improving the knowledge of the genetic architecture of resistance to gastrointestinal nematode in Santa Ines sheep.
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Affiliation(s)
- Nedenia Bonvino Stafuzza
- Sustainable Livestock Research Center, Animal Science Institute, 15130-000 São José do Rio Preto, SP, Brazil.
| | - Ana Claudia de Freitas
- São Paulo Agency of Agribusiness and Technology, Animal Science Institute, 13380-011 Nova Odessa, SP, Brazil; Agricultural Research Agency of the State of Minas Gerais, 38709-899 Patos de Minas, MG, Brazil
| | - Marina B Mioto
- Sustainable Livestock Research Center, Animal Science Institute, 15130-000 São José do Rio Preto, SP, Brazil
| | | | | | - Victor Breno Pedrosa
- Department of Animal Science, State University of Ponta Grossa, 84030-900 Ponta Grossa, PR, Brazil
| | - Ricardo Lopes Dias da Costa
- São Paulo Agency of Agribusiness and Technology, Animal Science Institute, 13380-011 Nova Odessa, SP, Brazil
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da Silva Neto JB, Peripoli E, Pereira ASC, Stafuzza NB, Lôbo RB, Fukumasu H, Ferraz JBS, Baldi F. Weighted genomic prediction for growth and carcass-related traits in Nelore cattle. Anim Genet 2023; 54:271-283. [PMID: 36856051 DOI: 10.1111/age.13310] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 03/02/2023]
Abstract
This study aimed to assess the impact of differential weighting in genomic regions harboring candidate causal loci on the genomic prediction accuracy and dispersion for growth and carcass-related traits in Nelore cattle. The dataset contained 168 793 phenotypic records for adjusted weight at 450 days of age (W450), 83 624 for rib eye area (REA), 24 480 for marbling (MAR) and 82 981 for subcutaneous backfat thickness (BFT) and rump fat thickness (RFT). The pedigree harbored information from 244 254 animals born between 1977 and 2016, including 6283 sires and 50 742 dams. Animals (n = 7769) were genotyped with the low-density panel (Clarifide® Nelore 3.0), and the genotypes were imputed to a panel containing 735 044 markers. A linear animal model was applied to estimate the genetic parameters and to perform the weighted single-step genome-wide association study (WssGWAS). A total of seven models for genomic prediction were evaluated combining the SNP weights obtained in the iterations of the WssGWAS and the candidate QTL. The heritability estimated for W450 (0.35) was moderate, and for carcass-related traits, the estimates were moderate for REA (0.27), MAR (0.28) and RFT (0.28), and low for BFT (0.18). The prediction accuracy for W450 incorporating reported QTL previously described in the literature along with different SNPs weights was like those described for the default ssGBLUP model. The use of the ssGWAS to weight the SNP effects displayed limited advantages for the REA prediction accuracy. Comparing the ssGBLUP with the BLUP model, a meaningful improvement in the prediction accuracy from 0.09 to 0.63 (700%) was observed for MAR. The highest prediction accuracy was obtained for BFT and RFT in all evaluated models. The application of information obtained from the WssGWAS is an alternative to reduce the genomic prediction dispersion for growth and carcass-related traits, except for MAR. Furthermore, the results obtained herein pointed out that is possible to improve the prediction accuracy and reduce the genomic prediction dispersion for growth and carcass-related traits in young animals.
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Affiliation(s)
- João Barbosa da Silva Neto
- Department of Animal Science, São Paulo State University - Júlio de Mesquita Filho (UNESP), Jaboticabal, Brazil
| | - Elisa Peripoli
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Angelica S C Pereira
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | | | - Raysildo B Lôbo
- National Association of Breeders and Researchers, Ribeirão Preto, Brazil
| | - Heigde Fukumasu
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - José Bento Sterman Ferraz
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Fernando Baldi
- Department of Animal Science, São Paulo State University - Júlio de Mesquita Filho (UNESP), Jaboticabal, Brazil
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Peripolli E, Stafuzza NB, Machado MA, do Carmo Panetto JC, do Egito AA, Baldi F, da Silva MVGB. Assessment of copy number variants in three Brazilian locally adapted cattle breeds using whole-genome re-sequencing data. Anim Genet 2023; 54:254-270. [PMID: 36740987 DOI: 10.1111/age.13298] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 12/13/2021] [Accepted: 01/13/2023] [Indexed: 02/07/2023]
Abstract
Further characterization of genetic structural variations should strongly focus on small and endangered local breeds given their role in unraveling genes and structural variants underlying selective pressures and phenotype variation. A comprehensive genome-wide assessment of copy number variations (CNVs) based on whole-genome re-sequencing data was performed on three Brazilian locally adapted cattle breeds (Caracu Caldeano, Crioulo Lageano, and Pantaneiro) using the ARS-UCD1.2 genome assembly. Data from 36 individuals with an average coverage depth of 14.07× per individual was used. A total of 24 945 CNVs were identified distributed among the breeds (Caracu Caldeano = 7285, Crioulo Lageano = 7297, and Pantaneiro = 10 363). Deletion events were 1.75-2.07-fold higher than duplications, and the total length of CNVs is composed mostly of a high number of segments between 10 and 30 kb. CNV regions (CNVRs) are not uniformly scattered throughout the genomes (n = 463), and 105 CNVRs were found overlapping among the studied breeds. Functional annotation of the CNVRs revealed variants with high consequence on protein sequence harboring relevant genes, in which we highlighted the BOLA-DQB, BOLA-DQA5, CD1A, β-defensins, PRG3, and ULBP21 genes. Enrichment analysis based on the gene list retrieved from the CNVRs disclosed over-represented terms (p < 0.01) strongly associated with immunity and cattle resilience to harsh environments. Additionally, QTL associated with body conformation and dairy-related traits were also unveiled within the CNVRs. These results provide better understanding of the selective forces shaping the genome of such cattle breeds and identify traces of natural selection pressures by which these populations have been exposed to challenging environmental conditions.
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Affiliation(s)
- Elisa Peripolli
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil
| | | | | | | | | | - Fernando Baldi
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil
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Pires BV, Freitas AC, Klein JL, de Melo TP, Stafuzza NB, de Paz CCP. Meta-analysis and meta-regression of core body temperature in taurine and zebuine cattle under different environmental conditions. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.105104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Berton MP, de Lemos MVA, Stafuzza NB, Simielli Fonseca LF, Silva DBDS, Peripolli E, Pereira ASC, Magalhães AFB, Albuquerque LG, Baldi F. Integration analyses of structural variations and differential gene expression associated with beef fatty acid profile in Nellore cattle. Anim Genet 2022; 53:570-582. [PMID: 35811456 DOI: 10.1111/age.13242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 06/06/2022] [Accepted: 06/22/2022] [Indexed: 11/26/2022]
Abstract
This study aimed to integrate analyses of structural variations and differentially expressed genes (DEGs) associated with the beef fatty acid (FA) profile in Nellore cattle. Copy numbers variation (CNV) detection was performed using the penncnv algorithm and CNVRuler software in 3794 genotyped animals through the High-Density Bovine BeadChip. In order to perform the genomic wide association study (GWAS), a total of 963 genotyped animals were selected to obtain the intramuscular lipid concentration and quantify the beef FA profile. A total of 48 animals belonging to the same farm and management lot were extracted from the 963 genotyped and phenotyped animals to carry out the transcriptomic and differentially expressed gene analyses. The GWAS with extreme groups of FA profiles was performed using a logistic model. A total of 43, 42, 66 and 35 significant CNV regions (p < 0.05) for saturated, monounsaturated, polyunsaturated and omega 3 and 6 fatty acids were identified respectively. The paired-end sequencing of 48 samples was performed using the Illumina HiSeq2500 platform. Real-time quantitative PCR was used to validate the DEGs identified by RNA-seq analysis. The results showed several DEGs associated with the FA profile of Longissimus thoracis, such as BSCL2 and SAMD8. Enriched terms as the cellular response to corticosteroid (GO:0071384) and glucocorticoid stimulus (GO:0071385) could be highlighted. The identification of structural variations harboring candidate genes for beef FA must contribute to the elucidation of the genetic basis that determines the beef FA composition of intramuscular fat in Nellore cattle. Our results will contribute to the identification of potential biomarkers for complex phenotypes, such as the FA profile, to improve the reliability of the genomic predictions including pre-selected variants using differentiated weighting in the genomic models.
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Affiliation(s)
- Mariana Piatto Berton
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Brazil
| | | | | | | | | | - Elisa Peripolli
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Brazil
| | - Angélica S C Pereira
- Departamento de Nutrição e Produção Animal, Universidade de São Paulo, Faculdade de Medicina Veterinária e Zootecnia, Pirassununga, Brazil
| | - Ana Fabricia Braga Magalhães
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Brazil
| | - Lucia G Albuquerque
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Brazil
| | - Fernando Baldi
- Departamento de Zootecnia, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Brazil
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Freitas LAD, Savegnago RP, Menegatto LS, Bem RDD, Stafuzza NB, Paz ACARD, Pires BV, Costa RLDD, Paz CCPD. Cluster analysis to explore additive-genetic patterns for the identification of sheep resistant, resilient and susceptible to gastrointestinal nematodes. Vet Parasitol 2022; 301:109640. [PMID: 34973595 DOI: 10.1016/j.vetpar.2021.109640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/30/2022]
Abstract
Infection caused by gastrointestinal nematodes is an important issue for animal health and production. Controlling worm infections improves the sustainability of the sheep industry. Genetic selection of animals that are resistant to gastrointestinal nematodes is another strategy to render sheep production more sustainable by decreasing the use of anthelmintics. The aims of this study were (1) to explore the additive-genetic pattern of EBVs for Famacha© (FAM), packed-cell volume (PVC), and fecal egg counts (FEC) of Santa Ines sheep, (2) to propose a classification of animals that are resistant, resilient and susceptible to gastrointestinal nematodes based on their additive-genetic patterns, and (3) to identify the most suitable animals for selection based on their genetic pattern. A dataset of 2,241 records from 747 animals was used to predict the breeding values for indicator traits of resistance to gastrointestinal nematodes with THRGIBBS1F90 and to carry out cluster analyses was used R software. Three clusters of animals were found in the population using hierarchical cluster analysis of the breeding values for FAM, PCV and FEC. Each cluster was characterized by different additive-genetic patterns identified by k-means non-hierarchical cluster analysis. Among a total of 747 animals, 196 were classified as resistant, 288 as resilient, and 263 as susceptible. Cluster analysis is a valuable tool for data screening that permits to evaluate only selection candidates based on their additive-genetic pattern for gastrointestinal nematode resistance. EBVs for FEC were decisive to divide the population into resilient, resistant and susceptible animals. It is also important to include the EBVs for PCV and FAM to adequately distinguish resistant from resilient animals. Finally, the resistant cluster consisted of the most desirable animals to be used as selection candidates in order to genetically improve resistance to infection with gastrointestinal nematodes. This cluster contained animals with the most appropriate additive-genetic pattern to achieve the breeding goal, with positive breeding values for PCV and negative breeding values for FAM and FEC.
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Affiliation(s)
- Luara Afonso de Freitas
- University of Sao Paulo, Department of Genetics, Ribeirão Preto, São Paulo, 14049-900, Brazil.
| | | | | | - Ricardo Dutra do Bem
- Instituto de Zootecnia, Beef Cattle Research Center, Animal Science Institute, Sertãozinho, São Paulo, 14174-000, Brazil.
| | - Nedenia Bonvino Stafuzza
- Instituto de Zootecnia, Beef Cattle Research Center, Animal Science Institute, Sertãozinho, São Paulo, 14174-000, Brazil.
| | | | - Bianca Vilela Pires
- University of Sao Paulo, Department of Genetics, Ribeirão Preto, São Paulo, 14049-900, Brazil.
| | | | - Claudia Cristina Paro de Paz
- University of Sao Paulo, Department of Genetics, Ribeirão Preto, São Paulo, 14049-900, Brazil; Instituto de Zootecnia, Beef Cattle Research Center, Animal Science Institute, Sertãozinho, São Paulo, 14174-000, Brazil.
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Kava R, Peripolli E, Berton MP, Lemos M, Lobo RB, Stafuzza NB, Pereira AS, Baldi F. Genome-wide structural variations in Brazilian Senepol cattle, a tropically adapted taurine breed. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Amorim ST, Stafuzza NB, Kluska S, Peripolli E, Pereira ASC, Muller da Silveira LF, de Albuquerque LG, Baldi F. Genome-wide interaction study reveals epistatic interactions for beef lipid-related traits in Nellore cattle. Anim Genet 2021; 53:35-48. [PMID: 34407235 DOI: 10.1111/age.13124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2021] [Indexed: 11/27/2022]
Abstract
Gene-gene interactions cause hidden genetic variation in natural populations and could be responsible for the lack of replication that is typically observed in complex traits studies. This study aimed to identify gene-gene interactions using the empirical Hilbert-Schmidt Independence Criterion method to test for epistasis in beef fatty acid profile traits of Nellore cattle. The dataset contained records from 963 bulls, genotyped using a 777 962k SNP chip. Meat samples of Longissimus muscle, were taken to measure fatty acid composition, which was quantified by gas chromatography. We chose to work with the sums of saturated (SFA), monounsaturated (MUFA), polyunsaturated (PUFA), omega-3 (OM3), omega-6 (OM6), SFA:PUFA and OM3:OM6 fatty acid ratios. The SNPs in the interactions where P < 10 - 8 were mapped individually and used to search for candidate genes. Totals of 602, 3, 13, 23, 13, 215 and 169 candidate genes for SFAs, MUFAs, PUFAs, OM3s, OM6s and SFA:PUFA and OM3:OM6 ratios were identified respectively. The candidate genes found were associated with cholesterol, lipid regulation, low-density lipoprotein receptors, feed efficiency and inflammatory response. Enrichment analysis revealed 57 significant GO and 18 KEGG terms ( P < 0.05), most of them related to meat quality and complementary terms. Our results showed substantial genetic interactions associated with lipid profile, meat quality, carcass and feed efficiency traits for the first time in Nellore cattle. The knowledge of these SNP-SNP interactions could improve understanding of the genetic and physiological mechanisms that contribute to lipid-related traits and improve human health by the selection of healthier meat products.
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Affiliation(s)
- S T Amorim
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no, Jaboticabal, CEP 14884-900, Brazil
| | - N B Stafuzza
- Instituto de Zootecnia - Centro de Pesquisa em Bovinos de Corte, Rodovia Carlos Tonanni, Km94, Sertãozinho, 14174-000, Brazil
| | - S Kluska
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no, Jaboticabal, CEP 14884-900, Brazil
| | - E Peripolli
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no, Jaboticabal, CEP 14884-900, Brazil
| | - A S C Pereira
- Faculdade de Zootecnia e Engenharia de Alimentos, Núcleo de Apoio à Pesquisa em Melhoramento Animal, Biotecnologia e Transgenia, Universidade de São Paulo, Rua Duque de Caxias Norte, 225, Pirassununga, CEP 13635-900, Brazil
| | - L F Muller da Silveira
- Faculdade de Zootecnia e Engenharia de Alimentos, Núcleo de Apoio à Pesquisa em Melhoramento Animal, Biotecnologia e Transgenia, Universidade de São Paulo, Rua Duque de Caxias Norte, 225, Pirassununga, CEP 13635-900, Brazil
| | - L G de Albuquerque
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no, Jaboticabal, CEP 14884-900, Brazil
| | - F Baldi
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no, Jaboticabal, CEP 14884-900, Brazil
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Berton MP, de Antunes Lemos MV, Seleguim Chud TC, Bonvino Stafuzza N, Kluska S, Amorim ST, Silva Ferlin Lopes L, Cravo Pereira AS, Bickhart D, Liu G, Galvão de Albuquerque L, Baldi F. Genome-wide association study between copy number variation regions and carcass- and meat-quality traits in Nellore cattle. Anim Prod Sci 2021. [DOI: 10.1071/an20275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Context
Indicine breeds are the main source of beef products in tropical and subtropical regions. However, genetic improvement for carcass- and meat-quality traits in zebu cattle have been limited and genomics studies concerning structural variations that influence these traits are essential.
Aim
The aim of this study was to perform a genome-wide association study between copy number variation regions (CNVRs) and carcass- and meat quality-traits in Nellore cattle.
Methods
In total, 3794 animals, males and females included, were genotyped using a 777962 single-nucleotide polymorphism platform of BovineHD BeadChip (777k; Illumina Inc.). Of these, 1751 Nellore bulls were slaughtered at 24 months of age for further carcass beef analysis. The following traits were studied: beef tenderness, marbling, rib-eye area, backfat thickness and meat colour (lightness, redness and yellowness). The CNV detection was conducted through PennCNV software. The association analyses were performed using CNVRuler software.
Key results
Several identified genomic regions were linked to quantitative trait loci associated with fat deposition (FABP7) and lipid metabolism (PPARA; PLA2 family; BCHE), extracellular matrix (INS; COL10A1), contraction (SLC34A3; TRDN) and muscle development (CAPZP). The gene-enrichment analyses highlighted biological mechanisms directly related to the metabolism and synthesis of lipids and fatty acids.
Conclusions
The large number of potential candidate genes identified within the CNVRs, as well as the functions and pathways identified, should help better elucidate the genetic mechanisms involved in the expression of beef and carcass traits in Nellore cattle. Several CNVRs harboured genes that might have a functional impact to improve the beef and carcass traits.
Implications
The results obtained contribute to upgrade the sensorial and organoleptic attributes of Nellore cattle and make feasible the genetic improvement of carcass- and meat-quality traits.
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Vilela Pires B, de Freitas LA, Voltareli da Silva G, Brasil Garcia Pimenta Neves Pereira Lima S, dos Santos Gonçalves Cyrillo JN, Bonvino Stafuzza N, Pereira de Lima ML, Paro de Paz CC. Influence of calf vigour and suckling assistance from birth to weaning in Guzerá beef cattle. Anim Prod Sci 2021. [DOI: 10.1071/an20056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context
Maternal ability, cow nutrition, and calf sex are factors that affect beef cattle production in extensive systems. The Guzerá cattle is an important breed in Brazil, where satisfactory growth rates are reported; however, studies on post-parturition calf and cow behaviour are scarce.
Aims
This study aimed to identify the influence of vigour at birth (ability to stand and suckle without assistance) and human assistance in colostrum intake (HA) on the haematological profile, cortisol concentration, and growth until weaning of Guzerá beef calf.
Methods
The following traits were observed in 73 male and 83 female calves: cow age at calving, sex, birthweight, vigour, HA, haematological profile, cortisol concentration, bodyweight at 120 days (W120), weaning weight, average daily gain and mortality. Variance analysis was performed using the general linear model procedure of the SAS software.
Key results
Haematocrit (P = 0.04) and red blood cells (P = 0.004) were higher in calves requiring HA. Cortisol was also higher (P = 0.03) in calves that required HA (81.34 ng/mL × 59.40 ng/mL). The weaning weight and average daily gain were higher (P < 0.05) in calves that did not require HA and showed good vigour (200.38 kg and 0.83 kg/day respectively) than in calves that required HA and showed good vigour (163.7 kg and 0.68 kg/day respectively). The mortality rate was higher in calves that showed poor vigour at birth (25%).
Conclusions
Both vigour and the need for HA are important traits that should be evaluated during the development of newborn calves. These assessments in the herd can contribute to minimise the mortality rate and maximise the health and weight gain until weaning of beef calves.
Implications
Few studies have reported the role of vigour and colostrum intake in the development of calves. Despite the difficulty of human interference in extensive cattle farming, the calf vigour combined with human assistance at birth can minimise the losses and increase the performance of beef cattle.
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13
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Olivieri BF, Braz CU, Brito Lopes F, Peripolli E, Medeiros de Oliveira Silva R, Ruegger Pereira da Silva Corte R, Albuquerque LGD, Pereira ASC, Stafuzza NB, Baldi F. Differentially expressed genes identified through RNA-seq with extreme values of principal components for beef fatty acid in Nelore cattle. J Anim Breed Genet 2020; 138:80-90. [PMID: 32424857 DOI: 10.1111/jbg.12483] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/13/2020] [Accepted: 04/22/2020] [Indexed: 12/13/2022]
Abstract
The aim of this study was to identify differentially expressed genes (DEG) in the Longissimus thoracis muscle of Nelore cattle related to fatty acid (FA) profile through RNA sequencing and principal component analysis (PCA). Two groups of 10 animals each were selected containing PC1 and PC2 extreme DEG values (HIGH × LOW) for each FA group. The intramuscular fat (IMF) was compared between cluster groups by ANOVA, and only the sum of monounsaturated FA (MUFA) and ω3 showed significant differences (p < .05). Interestingly, the highest percentage (95%) of phenotypic variation explained by the sum of the first two PC was observed for ω3, which also displayed the lowest number of DEG (n = 1). The lowest percentage (59%) was observed for MUFA, which also revealed the largest number of DEG (n = 66). Since only MUFA and ω3 exhibited significant differences between cluster groups, we can conclude that the differences observed for the remaining groups are not due to the percentage of IMF. Several genes that have been previously associated with meat quality and FA traits were identified as DEG in this study. The functional analysis revealed one KEGG pathway and eight GO terms as significant (p < .05), in which we highlighted the purine metabolism, glycolytic process, adenosine triphosphate binding and bone development. These results strongly contribute to the knowledge of the biological mechanisms involved in meat FA profile of Nelore cattle.
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Affiliation(s)
- Bianca Ferreira Olivieri
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Jaboticabal, Brazil
| | - Camila Urbano Braz
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Jaboticabal, Brazil
| | - Fernando Brito Lopes
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Jaboticabal, Brazil.,Embrapa Cerrados, Brasilia, Brazil
| | - Elisa Peripolli
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Jaboticabal, Brazil
| | | | | | - Lucia Galvão de Albuquerque
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Jaboticabal, Brazil
| | - Angélica Simone Cravo Pereira
- Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Nutrição e Produção Animal, Universidade de São Paulo (USP), Pirassununga, Brazil
| | | | - Fernando Baldi
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Jaboticabal, Brazil
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14
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Stafuzza NB, Costa E Silva EVD, Silva RMDO, Costa Filho LCCD, Barbosa FB, Macedo GG, Lobo RB, Baldi F. Genome-wide association study for age at puberty in young Nelore bulls. J Anim Breed Genet 2019; 137:234-244. [PMID: 31515857 DOI: 10.1111/jbg.12438] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/12/2019] [Accepted: 08/13/2019] [Indexed: 12/25/2022]
Abstract
Selection for bulls that would reach puberty early reduces the generation interval and increases fertility and herd productivity. Despite its economic importance, there are few QTL associated with age at puberty described in the literature. In this study, a weighted single-step genome-wide association study was performed to detect genomic regions and putative candidate genes related to age at puberty in young Nelore bulls. Several protein-coding genes related to spermatogenesis functions were identified within the genomic regions that explain more than 0.5% of the additive genetic variance for age at puberty in Nelore bulls, such as ADAM11, BRCA1, CSNK2A, CREBBP, MEIOC, NDRG2, NECTIN3, PARP2, PARP9, PRSS21, RAD51C, RNASE4, SLX4, SPA17, TEX14, TIMP2 and TRIP13 gene. Enrichment analysis by DAVID also revealed several GO terms related to spermatogenesis such as DNA replication (GO:0006260), male meiosis I (GO:0007141), double-strand break repair (GO:0006302), base excision repair (GO:0006284), apoptotic process (GO:0006915), cell-cell adhesion (GO: 0098609) and focal adhesion (GO:0005925). The heritability for age at puberty shows that this trait can be improved based on traditional EBV selection. Adding genomic information to the system helps to elucidate genes and molecular mechanisms controlling the sexual precocity and could help to predict sexual precocity in Nelore bulls with greater accuracy at younger age, which would speed up the breeding programme for this breed.
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Affiliation(s)
| | - Eliane Vianna da Costa E Silva
- Laboratório de Reprodução Animal, Faculdade de Medicina Veterinária e Zootecnia (FAMEZ), Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, Brazil
| | | | - Luiz Carlos Cesar da Costa Filho
- Laboratório de Reprodução Animal, Faculdade de Medicina Veterinária e Zootecnia (FAMEZ), Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, Brazil.,PROCRIAR Assistência Veterinária, Campo Grande, Brazil
| | - Fernanda Battistotti Barbosa
- Laboratório de Reprodução Animal, Faculdade de Medicina Veterinária e Zootecnia (FAMEZ), Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, Brazil.,PROCRIAR Assistência Veterinária, Campo Grande, Brazil
| | - Gustavo Guerino Macedo
- Laboratório de Reprodução Animal, Faculdade de Medicina Veterinária e Zootecnia (FAMEZ), Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, Brazil
| | - Raysildo B Lobo
- Associação Nacional dos Criadores e Pesquisadores (ANCP), Ribeirão Preto, Brazil
| | - Fernando Baldi
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista Julio de Mesquita Filho (UNESP), Jaboticabal, Brazil
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15
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Peripolli E, Stafuzza NB, Amorim ST, Lemos MVA, Grigoletto L, Kluska S, Ferraz JBS, Eler JP, Mattos EC, Baldi F. Genome‐wide scan for runs of homozygosity in the composite Montana Tropical
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beef cattle. J Anim Breed Genet 2019; 137:155-165. [DOI: 10.1111/jbg.12428] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Elisa Peripolli
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia UNESP Univ Estadual Paulista Júlio de Mesquita Filho Jaboticabal Brazil
| | | | - Sabrina Thaise Amorim
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia UNESP Univ Estadual Paulista Júlio de Mesquita Filho Jaboticabal Brazil
| | - Marcos Vinícius Antunes Lemos
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia UNESP Univ Estadual Paulista Júlio de Mesquita Filho Jaboticabal Brazil
| | - Laís Grigoletto
- Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária Universidade de São Paulo Pirassununga Brazil
| | - Sabrina Kluska
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia UNESP Univ Estadual Paulista Júlio de Mesquita Filho Jaboticabal Brazil
| | - José Bento Sterman Ferraz
- Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária Universidade de São Paulo Pirassununga Brazil
| | - Joanir Pereira Eler
- Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária Universidade de São Paulo Pirassununga Brazil
| | - Elisângela Chicaroni Mattos
- Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária Universidade de São Paulo Pirassununga Brazil
| | - Fernando Baldi
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia UNESP Univ Estadual Paulista Júlio de Mesquita Filho Jaboticabal Brazil
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Stafuzza NB, Silva RMDO, Fragomeni BDO, Masuda Y, Huang Y, Gray K, Lourenco DAL. A genome-wide single nucleotide polymorphism and copy number variation analysis for number of piglets born alive. BMC Genomics 2019; 20:321. [PMID: 31029102 PMCID: PMC6487013 DOI: 10.1186/s12864-019-5687-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 04/11/2019] [Indexed: 12/19/2022] Open
Abstract
Background In this study we integrated the CNV (copy number variation) and WssGWAS (weighted single-step approach for genome-wide association) analyses to increase the knowledge about number of piglets born alive, an economically important reproductive trait with significant impact on production efficiency of pigs. Results A total of 3892 samples were genotyped with the Porcine SNP80 BeadChip. After quality control, a total of 57,962 high-quality SNPs from 3520 Duroc pigs were retained. The PennCNV algorithm identified 46,118 CNVs, which were aggregated by overlapping in 425 CNV regions (CNVRs) ranging from 2.5 Kb to 9718.4 Kb and covering 197 Mb (~ 7.01%) of the pig autosomal genome. The WssGWAS identified 16 genomic regions explaining more than 1% of the additive genetic variance for number of piglets born alive. The overlap between CNVR and WssGWAS analyses identified common regions on SSC2 (4.2–5.2 Mb), SSC3 (3.9–4.9 Mb), SSC12 (56.6–57.6 Mb), and SSC17 (17.3–18.3 Mb). Those regions are known for harboring important causative variants for pig reproductive traits based on their crucial functions in fertilization, development of gametes and embryos. Functional analysis by the Panther software identified 13 gene ontology biological processes significantly represented in this study such as reproduction, developmental process, cellular component organization or biogenesis, and immune system process, which plays relevant roles in swine reproductive traits. Conclusion Our research helps to improve the understanding of the genetic architecture of number of piglets born alive, given that the combination of GWAS and CNV analyses allows for a more efficient identification of the genomic regions and biological processes associated with this trait in Duroc pigs. Pig breeding programs could potentially benefit from a more accurate discovery of important genomic regions. Electronic supplementary material The online version of this article (10.1186/s12864-019-5687-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nedenia Bonvino Stafuzza
- Department of Exact Science, School of Agricultural and Veterinarian Sciences (FCAV), Sao Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil. .,Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA.
| | - Rafael Medeiros de Oliveira Silva
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA.,National Center for Cool and Cold Water Aquaculture (NCCCWA), Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, USA
| | | | - Yutaka Masuda
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Yijian Huang
- Smithfield Premium Genetics Group, Rose Hill, NC, USA
| | - Kent Gray
- Smithfield Premium Genetics Group, Rose Hill, NC, USA
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17
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Freitas LAD, Savegnago RP, Grupioni NV, Ramos SB, Stafuzza NB, Figueiredo EAPD, Schmidt GS, Ledur MC, Munari DP. Reduced-rank estimation of genetic parameters for egg production traits and cluster analyses with predicted breeding values. ACTA AGR SCAND A-AN 2019. [DOI: 10.1080/09064702.2019.1580308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Luara Afonso de Freitas
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista ‘Júlio de Mesquita Filho’, Jaboticabal, Brazil
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Rodrigo Pelicioni Savegnago
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista ‘Júlio de Mesquita Filho’, Jaboticabal, Brazil
- Instituto de Zootecnia, Centro de Pesquisa em Bovinos de Corte, Sertãozinho, Brazil
| | - Natalia Vinhal Grupioni
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista ‘Júlio de Mesquita Filho’, Jaboticabal, Brazil
| | | | - Nedenia Bonvino Stafuzza
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista ‘Júlio de Mesquita Filho’, Jaboticabal, Brazil
| | | | | | | | - Danisio Prado Munari
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista ‘Júlio de Mesquita Filho’, Jaboticabal, Brazil
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18
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Amorim ST, Kluska S, Berton MP, de Lemos MVA, Peripolli E, Stafuzza NB, Martin JF, Álvarez MS, Gaviña BV, Toro MA, Banchero G, Oliveira PS, Grigoletto L, Eler JP, Baldi F, Ferraz JBS. Genomic study for maternal related traits in Santa Inês sheep breed. Livest Sci 2018. [DOI: 10.1016/j.livsci.2018.09.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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19
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Peripolli E, Metzger J, de Lemos MVA, Stafuzza NB, Kluska S, Olivieri BF, Feitosa FLB, Berton MP, Lopes FB, Munari DP, Lôbo RB, Magnabosco CDU, Di Croce F, Osterstock J, Denise S, Pereira ASC, Baldi F. Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits. BMC Genomics 2018; 19:680. [PMID: 30223795 PMCID: PMC6142381 DOI: 10.1186/s12864-018-5060-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 09/07/2018] [Indexed: 12/20/2022] Open
Abstract
Background The aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages. It attempts also to compare estimates of inbreeding calculated from ROH (FROH), genomic relationship matrix (FGRM), and pedigree-based coefficient (FPED). Results The average number of ROH per animal was 55.15 ± 13.01 with an average size of 3.24 Mb. The Nellore genome is composed mostly by a high number of shorter segments accounting for 78% of all ROH, although the proportion of the genome covered by them was relatively small. The genome autozygosity proportion indicates moderate to high inbreeding levels for classical standards, with an average value of 7.15% (178.70 Mb). The average of FPED and FROH, and their correlations (− 0.05 to 0.26) were low. Estimates of correlation between FGRM-FPED was zero, while the correlation (− 0.01 to − 0.07) between FGRM-FROH decreased as a function of ROH length, except for FROH > 8Mb (− 0.03). Overall, inbreeding coefficients were not high for the genotyped animals. Autozygosity islands were evident across the genome (n = 62) and their genomic location did not largely differ within lineages. Enriched terms (p < 0.01) associated with defense response to bacteria (GO:0042742), immune complex reaction (GO:0045647), pregnancy-associated glycoproteins genes (GO:0030163), and organism growth (GO:0040014) were described within the autozygotic islands. Conclusions Low FPED-FROH correlation estimates indicate that FPED is not the most suitable method for capturing ancient inbreeding when the pedigree does not extend back many generations and FROH should be used instead. Enriched terms (p < 0.01) suggest a strong selection for immune response. Non-overlapping islands within the lineages greatly explain the mechanism underlying selection for functionally important traits in Nellore cattle. Electronic supplementary material The online version of this article (10.1186/s12864-018-5060-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elisa Peripolli
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil.
| | - Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, 30559, Hannover, Germany
| | - Marcos Vinícius Antunes de Lemos
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Nedenia Bonvino Stafuzza
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Sabrina Kluska
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Bianca Ferreira Olivieri
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Fabieli Louise Braga Feitosa
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Mariana Piatto Berton
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Fernando Brito Lopes
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Danísio Prado Munari
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Raysildo Barbosa Lôbo
- Associação Nacional de Criadores e Pesquisadores (ANCP), Ribeirão Preto, 14020-230, Brazil
| | | | | | | | | | | | - Fernando Baldi
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
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20
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Stafuzza NB, Silva RMDO, Peripolli E, Bezerra LAF, Lôbo RB, Magnabosco CDU, Di Croce FA, Osterstock JB, Munari DP, Lourenco DAL, Baldi F. Genome-wide association study provides insights into genes related with horn development in Nelore beef cattle. PLoS One 2018; 13:e0202978. [PMID: 30161212 PMCID: PMC6116989 DOI: 10.1371/journal.pone.0202978] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 08/13/2018] [Indexed: 11/28/2022] Open
Abstract
The causal mutation for polledness in Nelore (Bos taurus indicus) breed seems to have appeared first in Brazil in 1957. The expression of the polled trait is known to be ruled by a few groups of alleles in taurine breeds; however, the genetic basis of this trait in indicine cattle is still unclear. The aim of this study was to identify genomic regions associated with the hornless trait in a commercial Nelore population. A total of 107,294 animals had phenotypes recorded and 2,238 were genotyped/imputed for 777k SNP. The weighted single-step approach for genome-wide association study (WssGWAS) was used to estimate the SNP effects and variances accounted for by 1 Mb sliding SNP windows. A centromeric region of chromosome 1 with 3.11 Mb size (BTA1: 878,631–3,987,104 bp) was found to be associated with hornless in the studied population. A total of 28 protein-coding genes are mapped in this region, including the taurine Polled locus and the IFNAR1, IFNAR2, IFNGR2, KRTAP11-1, MIS18A, OLIG1, OLIG2, and SOD1 genes, which expression can be related to the horn formation as described in literature. The functional enrichment analysis by DAVID tool revealed cytokine-cytokine receptor interaction, JAK-STAT signaling, natural killer cell mediated cytotoxicity, and osteoclast differentiation pathways as significant (P < 0.05). In addition, a runs of homozygosity (ROH) analysis identified a ROH island in polled animals with 2.47 Mb inside the region identified by WssGWAS. Polledness in Nelore cattle is associated with one region in the genome with 3.1 Mb size in chromosome 1. Several genes are harbored in this region, and they may act together in the determination of the polled/horned phenotype. Fine mapping the locus responsible for polled trait in Nelore breed and the identification of the molecular mechanisms regulating the horn growth deserve further investigation.
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Affiliation(s)
- Nedenia Bonvino Stafuzza
- Departamento de Ciencias Exatas, Faculdade de Ciencias Agrarias e Veterinarias (FCAV), Universidade Estadual Paulista Julio de Mesquita Filho (UNESP), Jaboticabal, Sao Paulo, Brazil
- Department of Animal and Dairy Science, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
| | - Rafael Medeiros de Oliveira Silva
- Department of Animal and Dairy Science, University of Georgia, Athens, Georgia, United States of America
- National Center for Cool and Cold Water Aquaculture (NCCCWA), Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Leetown, West Virginia, United States of America
| | - Elisa Peripolli
- Departamento de Zootecnia, Faculdade de Ciencias Agrarias e Veterinarias (FCAV), Universidade Estadual Paulista Julio de Mesquita Filho (UNESP), Jaboticabal, Sao Paulo, Brazil
| | - Luiz Antônio Framartino Bezerra
- Departamento de Genetica, Faculdade de Medicina de Ribeirao Preto (FMRP), Universidade de Sao Paulo (USP), Ribeirao Preto, Sao Paulo, Brazil
| | - Raysildo Barbosa Lôbo
- Associaçao Nacional dos Criadores e Pesquisadores (ANCP), Ribeirao Preto, Sao Paulo, Brazil
| | | | | | | | - Danísio Prado Munari
- Departamento de Ciencias Exatas, Faculdade de Ciencias Agrarias e Veterinarias (FCAV), Universidade Estadual Paulista Julio de Mesquita Filho (UNESP), Jaboticabal, Sao Paulo, Brazil
| | - Daniela A. Lino Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, Georgia, United States of America
| | - Fernando Baldi
- Departamento de Zootecnia, Faculdade de Ciencias Agrarias e Veterinarias (FCAV), Universidade Estadual Paulista Julio de Mesquita Filho (UNESP), Jaboticabal, Sao Paulo, Brazil
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Maiorano AM, Lourenco DL, Tsuruta S, Ospina AMT, Stafuzza NB, Masuda Y, Filho AEV, Cyrillo JNDSG, Curi RA, Silva JAIIDV. Assessing genetic architecture and signatures of selection of dual purpose Gir cattle populations using genomic information. PLoS One 2018; 13:e0200694. [PMID: 30071036 PMCID: PMC6071998 DOI: 10.1371/journal.pone.0200694] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 07/02/2018] [Indexed: 12/31/2022] Open
Abstract
Gir is one of the main cattle breeds raised in tropical South American countries. Strong artificial selection through its domestication resulted in increased genetic differentiation among the countries in recent years. Over the years, genomic studies in Gir have become more common. However, studies of population structure and signatures of selection in divergent Gir populations are scarce and need more attention to better understand genetic differentiation, gene flow, and genetic distance. Genotypes of 173 animals selected for growth traits and 273 animals selected for milk production were used in this study. Clear genetic differentiation between beef and dairy populations was observed. Different criteria led to genetic divergence and genetic differences in allele frequencies between the two populations. Gene segregation in each population was forced by artificial selection, promoting isolation, and increasing genetic variation between them. Results showed evidence of selective forces in different regions of the genome. A total of 282 genes were detected under selection in the test population based on the fixation index (Fst), integrated haplotype score (iHS), and cross-population extend haplotype homozygosity (XP-EHH) approaches. The QTL mapping identified 35 genes associated with reproduction, milk composition, growth, meat and carcass, health, or body conformation traits. The investigation of genes and pathways showed that quantitative traits associated to fertility, milk production, beef quality, and growth were involved in the process of differentiation of these populations. These results would support further investigations of population structure and differentiation in the Gir breed.
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Affiliation(s)
- Amanda Marchi Maiorano
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, Sao Paulo, Brazil
- * E-mail:
| | - Daniela Lino Lourenco
- Animal and Dairy Science, Animal Breeding and Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Shogo Tsuruta
- Animal and Dairy Science, Animal Breeding and Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Alejandra Maria Toro Ospina
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, Sao Paulo, Brazil
| | - Nedenia Bonvino Stafuzza
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, Sao Paulo, Brazil
| | - Yutaka Masuda
- Animal and Dairy Science, Animal Breeding and Genetics, University of Georgia, Athens, Georgia, United States of America
| | | | | | - Rogério Abdallah Curi
- Faculdade de Medicina Veterinária e Zootecnia, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, Sao Paulo, Brazil
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22
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Peripolli E, Stafuzza NB, Munari DP, Lima ALF, Irgang R, Machado MA, Panetto JCDC, Ventura RV, Baldi F, da Silva MVGB. Assessment of runs of homozygosity islands and estimates of genomic inbreeding in Gyr (Bos indicus) dairy cattle. BMC Genomics 2018; 19:34. [PMID: 29316879 PMCID: PMC5759835 DOI: 10.1186/s12864-017-4365-3] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 12/04/2017] [Indexed: 11/10/2022] Open
Abstract
Background Runs of homozygosity (ROH) are continuous homozygous segments of the DNA sequence. They have been applied to quantify individual autozygosity and used as a potential inbreeding measure in livestock species. The aim of the present study was (i) to investigate genome-wide autozygosity to identify and characterize ROH patterns in Gyr dairy cattle genome; (ii) identify ROH islands for gene content and enrichment in segments shared by more than 50% of the samples, and (iii) compare estimates of molecular inbreeding calculated from ROH (FROH), genomic relationship matrix approach (FGRM) and based on the observed versus expected number of homozygous genotypes (FHOM), and from pedigree-based coefficient (FPED). Results ROH were identified in all animals, with an average number of 55.12 ± 10.37 segments and a mean length of 3.17 Mb. Short segments (ROH1–2 Mb) were abundant through the genomes, which accounted for 60% of all segments identified, even though the proportion of the genome covered by them was relatively small. The findings obtained in this study suggest that on average 7.01% (175.28 Mb) of the genome of this population is autozygous. Overlapping ROH were evident across the genomes and 14 regions were identified with ROH frequencies exceeding 50% of the whole population. Genes associated with lactation (TRAPPC9), milk yield and composition (IRS2 and ANG), and heat adaptation (HSF1, HSPB1, and HSPE1), were identified. Inbreeding coefficients were estimated through the application of FROH, FGRM, FHOM, and FPED approaches. FPED estimates ranged from 0.00 to 0.327 and FROH from 0.001 to 0.201. Low to moderate correlations were observed between FPED-FROH and FGRM-FROH, with values ranging from −0.11 to 0.51. Low to high correlations were observed between FROH-FHOM and moderate between FPED-FHOM and FGRM-FHOM. Correlations between FROH from different lengths and FPED gradually increased with ROH length. Conclusions Genes inside ROH islands suggest a strong selection for dairy traits and enrichment for Gyr cattle environmental adaptation. Furthermore, low FPED-FROH correlations for small segments indicate that FPED estimates are not the most suitable method to capture ancient inbreeding. The existence of a moderate correlation between larger ROH indicates that FROH can be used as an alternative to inbreeding estimates in the absence of pedigree records. Electronic supplementary material The online version of this article (10.1186/s12864-017-4365-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elisa Peripolli
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Nedenia Bonvino Stafuzza
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Ciências Exatas, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Danísio Prado Munari
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Ciências Exatas, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil.,Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ), Lago Sul, 71605-001, Brazil
| | - André Luís Ferreira Lima
- Centro de Ciências Agrárias, Departamento de Zootecnia e Desenvolvimento Rural, Universidade Federal de Santa Catarina, Florianópolis, 88034-000, Brazil
| | - Renato Irgang
- Centro de Ciências Agrárias, Departamento de Zootecnia e Desenvolvimento Rural, Universidade Federal de Santa Catarina, Florianópolis, 88034-000, Brazil
| | - Marco Antonio Machado
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ), Lago Sul, 71605-001, Brazil.,Embrapa Gado de Leite, Juiz de Fora, 36038-330, Brazil
| | | | - Ricardo Vieira Ventura
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, 13635-900, Brazil.,Beef Improvement Opportunities, Elora, ON, N0B 1S0, Canada.,University of Guelph, Centre for Genetic Improvement of Livestock, ABScBG, Guelph, N1G 2W1, Canada
| | - Fernando Baldi
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil.,Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ), Lago Sul, 71605-001, Brazil
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Berton MP, de Oliveira Silva RM, Peripolli E, Stafuzza NB, Martin JF, Álvarez MS, Gavinã BV, Toro MA, Banchero G, Oliveira PS, Eler JP, Baldi F, Ferraz JBS. Genomic regions and pathways associated with gastrointestinal parasites resistance in Santa Inês breed adapted to tropical climate. J Anim Sci Biotechnol 2017; 8:73. [PMID: 28878894 PMCID: PMC5584554 DOI: 10.1186/s40104-017-0190-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 06/12/2017] [Indexed: 12/26/2022] Open
Abstract
Background The aim of this study was to estimate variance components and to identify genomic regions and pathways associated with resistance to gastrointestinal parasites, particularly Haemonchus contortus, in a breed of sheep adapted to tropical climate. Phenotypes evaluations were performed to verify resistance to gastrointestinal parasites, and were divided into two categories: i) farm phenotypes, assessing body condition score (BCS), degree of anemia assessed by the famacha chart (FAM), fur score (FS) and feces consistency (FC); and ii) lab phenotypes, comprising blood analyses for hematocrit (HCT), white blood cell count (WBC), red blood cell count (RBC), hemoglobin (HGB), platelets (PLT) and transformed (log10) egg per gram of feces (EPGlog). A total of 576 animals were genotyped with the Ovine SNP12k BeadChip (Illumina, Inc.), that contains 12,785 bialleleic SNP markers. The variance components were estimated using a single trait model by single step genomic BLUP procedure. Results The overall linkage disequilibrium (LD) mean between pairs of markers measured by r2 was 0.23. The overall LD mean between markers considering windows up to 10 Mb was 0.07. The mean LD between adjacent SNPs across autosomes ranged from 0.02 to 0.10. Heritability estimates were low for EPGlog (0.11), moderate for RBC (0.18), PLT (0.17) HCT (0.20), HGB (0.16) and WBC (0.22), and high for FAM (0.35). A total of 22, 21, 23, 20, 26, 25 and 23 windows for EPGlog for FAM, WBC, RBC, PLT, HCT and HGB traits were identified, respectively. Among the associated windows, 10 were shown to be common to HCT and HGB traits on OAR1, OAR2, OAR3, OAR5, OAR8 and OAR15. Conclusion The traits indicating gastrointestinal parasites resistance presented an adequate genetic variability to respond to selection in Santa Inês breed, and it is expected a higher genetic gain for FAM trait when compared to the others. The level of LD estimated for markers separated by less than 1 Mb indicated that the Ovine SNP12k BeadChip might be a suitable tool for identifying genomic regions associated with traits related to gastrointestinal parasite resistance. Several candidate genes related to immune system development and activation, inflammatory response, regulation of lymphocytes and leukocytes proliferation were found. These genes may help in the selection of animals with higher resistance to parasites. Electronic supplementary material The online version of this article (doi:10.1186/s40104-017-0190-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mariana Piatto Berton
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no, Jaboticabal, SP CEP 14884-900 Brazil
| | - Rafael Medeiros de Oliveira Silva
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no, Jaboticabal, SP CEP 14884-900 Brazil
| | - Elisa Peripolli
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no, Jaboticabal, SP CEP 14884-900 Brazil
| | - Nedenia Bonvino Stafuzza
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no, Jaboticabal, SP CEP 14884-900 Brazil
| | - Jesús Fernández Martin
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria INIA, Crta. de la Coruña, km 7,5 -, 28040 Madrid, Spain
| | - Maria Saura Álvarez
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria INIA, Crta. de la Coruña, km 7,5 -, 28040 Madrid, Spain
| | - Beatriz Villanueva Gavinã
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria INIA, Crta. de la Coruña, km 7,5 -, 28040 Madrid, Spain
| | - Miguel Angel Toro
- Departamento de Producción Agraria, School of Agricultural, Food and Byosystems Engineering, Universisdad Politécnica de Madrid, Campus Ciudad Universitaria Avda. Complutense 3 - Avda. Puerta Hierro, 28040 Madrid, Spain
| | - Georgget Banchero
- Instituto Nacional de Investigación Agropecuária (INIA), Ruta 50 Km. 12, Colonia, Uruguay
| | - Priscila Silva Oliveira
- Faculdade de Zootecnia e Engenharia de Alimentos, Nucleo de Apoio à Pesquisa em Melhoramento Animal, Biotecnologia e Transgenia, Universidade de São Paulo, Rua Duque de Caxias Norte, 225, Pirassununga, SP CEP 13635-900 Brazil
| | - Joanir Pereira Eler
- Faculdade de Zootecnia e Engenharia de Alimentos, Nucleo de Apoio à Pesquisa em Melhoramento Animal, Biotecnologia e Transgenia, Universidade de São Paulo, Rua Duque de Caxias Norte, 225, Pirassununga, SP CEP 13635-900 Brazil
| | - Fernando Baldi
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no, Jaboticabal, SP CEP 14884-900 Brazil
| | - José Bento Sterman Ferraz
- Faculdade de Zootecnia e Engenharia de Alimentos, Nucleo de Apoio à Pesquisa em Melhoramento Animal, Biotecnologia e Transgenia, Universidade de São Paulo, Rua Duque de Caxias Norte, 225, Pirassununga, SP CEP 13635-900 Brazil
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Buzanskas ME, Grossi DDA, Ventura RV, Schenkel FS, Chud TCS, Stafuzza NB, Rola LD, Meirelles SLC, Mokry FB, Mudadu MDA, Higa RH, da Silva MVGB, de Alencar MM, Regitano LCDA, Munari DP. Candidate genes for male and female reproductive traits in Canchim beef cattle. J Anim Sci Biotechnol 2017; 8:67. [PMID: 28852499 PMCID: PMC5569548 DOI: 10.1186/s40104-017-0199-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 07/13/2017] [Indexed: 01/20/2023] Open
Abstract
Background Beef cattle breeding programs in Brazil have placed greater emphasis on the genomic study of reproductive traits of males and females due to their economic importance. In this study, genome-wide associations were assessed for scrotal circumference at 210 d of age, scrotal circumference at 420 d of age, age at first calving, and age at second calving, in Canchim beef cattle. Data quality control was conducted resulting in 672,778 SNPs and 392 animals. Results Associated SNPs were observed for scrotal circumference at 420 d of age (435 SNPs), followed by scrotal circumference at 210 d of age (12 SNPs), age at first calving (six SNPs), and age at second calving (four SNPs). We investigated whether significant SNPs were within genic or surrounding regions. Biological processes of genes were associated with immune system, multicellular organismal process, response to stimulus, apoptotic process, cellular component organization or biogenesis, biological adhesion, and reproduction. Conclusions Few associations were observed for scrotal circumference at 210 d of age, age at first calving, and age at second calving, reinforcing their polygenic inheritance and the complexity of understanding the genetic architecture of reproductive traits. Finding many associations for scrotal circumference at 420 d of age in various regions of the Canchim genome also reveals the difficulty of targeting specific candidate genes that could act on fertility; nonetheless, the high linkage disequilibrium between loci herein estimated could aid to overcome this issue. Therefore, all relevant information about genomic regions influencing reproductive traits may contribute to target candidate genes for further investigation of causal mutations and aid in future genomic studies in Canchim cattle to improve the breeding program. Electronic supplementary material The online version of this article (doi:10.1186/s40104-017-0199-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marcos Eli Buzanskas
- Departamento de Zootecnia, Universidade Federal da Paraíba (UFPB), Areia, Paraíba 58397-000 Brazil
| | | | | | - Flavio Schramm Schenkel
- Department of Animal and Poultry Science, University of Guelph, Centre for Genetic Improvement of Livestock (CGIL), Guelph, ON N1G 2W1 Canada
| | - Tatiane Cristina Seleguim Chud
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, São Paulo 14884-900 Brazil
| | - Nedenia Bonvino Stafuzza
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, São Paulo 14884-900 Brazil
| | - Luciana Diniz Rola
- Departamento de Zootecnia, Núcleo de Pesquisa e Conservação de Cervídeos, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, São Paulo 14884-900 Brazil
| | | | - Fabiana Barichello Mokry
- Department of Genetics and Evolution, Federal University of São Carlos (UFSCar), São Carlos, São Paulo 13565-905 Brazil
| | | | | | | | | | | | - Danísio Prado Munari
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Jaboticabal, São Paulo 14884-900 Brazil
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Stafuzza NB, Zerlotini A, Lobo FP, Yamagishi MEB, Chud TCS, Caetano AR, Munari DP, Garrick DJ, Machado MA, Martins MF, Carvalho MR, Cole JB, Barbosa da Silva MVG. Single nucleotide variants and InDels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds. PLoS One 2017; 12:e0173954. [PMID: 28323836 PMCID: PMC5360315 DOI: 10.1371/journal.pone.0173954] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 03/01/2017] [Indexed: 11/18/2022] Open
Abstract
Whole-genome re-sequencing, alignment and annotation analyses were undertaken for 12 sires representing four important cattle breeds in Brazil: Guzerat (multi-purpose), Gyr, Girolando and Holstein (dairy production). A total of approximately 4.3 billion reads from an Illumina HiSeq 2000 sequencer generated for each animal 10.7 to 16.4-fold genome coverage. A total of 27,441,279 single nucleotide variations (SNVs) and 3,828,041 insertions/deletions (InDels) were detected in the samples, of which 2,557,670 SNVs and 883,219 InDels were novel. The submission of these genetic variants to the dbSNP database significantly increased the number of known variants, particularly for the indicine genome. The concordance rate between genotypes obtained using the Bovine HD BeadChip array and the same variants identified by sequencing was about 99.05%. The annotation of variants identified numerous non-synonymous SNVs and frameshift InDels which could affect phenotypic variation. Functional enrichment analysis was performed and revealed that variants in the olfactory transduction pathway was over represented in all four cattle breeds, while the ECM-receptor interaction pathway was over represented in Girolando and Guzerat breeds, the ABC transporters pathway was over represented only in Holstein breed, and the metabolic pathways was over represented only in Gyr breed. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Gyr, Girolando, Guzerat and Holstein breeding programs.
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Affiliation(s)
- Nedenia Bonvino Stafuzza
- Departamento de Ciências Exatas, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | | | | | | | - Tatiane Cristina Seleguim Chud
- Departamento de Ciências Exatas, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | | | - Danísio Prado Munari
- Departamento de Ciências Exatas, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Dorian J. Garrick
- Department of Animal Science, Iowa State University, Ames, Iowa, United States of America
| | | | | | - Maria Raquel Carvalho
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - John Bruce Cole
- United States Department of Agriculture, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, Maryland, United States of America
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Medeiros de Oliveira Silva R, Bonvino Stafuzza N, de Oliveira Fragomeni B, Miguel Ferreira de Camargo G, Matos Ceacero T, Noely dos Santos Gonçalves Cyrillo J, Baldi F, Augusti Boligon A, Zerlotti Mercadante ME, Lino Lourenco D, Misztal I, Galvão de Albuquerque L. Genome-Wide Association Study for Carcass Traits in an Experimental Nelore Cattle Population. PLoS One 2017; 12:e0169860. [PMID: 28118362 PMCID: PMC5261778 DOI: 10.1371/journal.pone.0169860] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 12/22/2016] [Indexed: 12/22/2022] Open
Abstract
The purpose of this study was to identify genomic regions associated with carcass traits in an experimental Nelore cattle population. The studied data set contained 2,306 ultrasound records for longissimus muscle area (LMA), 1,832 for backfat thickness (BF), and 1,830 for rump fat thickness (RF). A high-density SNP panel (BovineHD BeadChip assay 700k, Illumina Inc., San Diego, CA) was used for genotyping. After genomic data quality control, 437,197 SNPs from 761 animals were available, of which 721 had phenotypes for LMA, 669 for BF, and 718 for RF. The SNP solutions were estimated using a single-step genomic BLUP approach (ssGWAS), which calculated the variance for windows of 50 consecutive SNPs and the regions that accounted for more than 0.5% of the additive genetic variance were used to search for candidate genes. The results indicated that 12, 18, and 15 different windows were associated to LMA, BF, and RF, respectively. Confirming the polygenic nature of the studied traits, 43, 65, and 53 genes were found in those associated windows, respectively for LMA, BF, and RF. Among the candidate genes, some of them, which already had their functions associated with the expression of energy metabolism, were found associated with fat deposition in this study. In addition, ALKBH3 and HSD17B12 genes, which are related in fibroblast death and metabolism of steroids, were found associated with LMA. The results presented here should help to better understand the genetic and physiologic mechanism regulating the muscle tissue deposition and subcutaneous fat cover expression of Zebu animals. The identification of candidate genes should contribute for Zebu breeding programs in order to consider carcass traits as selection criteria in their genetic evaluation.
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Affiliation(s)
- Rafael Medeiros de Oliveira Silva
- School of Agricultural and Veterinarian Sciences, FCAV/ UNESP–Sao Paulo State University, Department of Animal Science, Jaboticabal-SP, Brazil
| | - Nedenia Bonvino Stafuzza
- School of Agricultural and Veterinarian Sciences, FCAV/ UNESP–Sao Paulo State University, Department of Animal Science, Jaboticabal-SP, Brazil
| | | | - Gregório Miguel Ferreira de Camargo
- School of Agricultural and Veterinarian Sciences, FCAV/ UNESP–Sao Paulo State University, Department of Animal Science, Jaboticabal-SP, Brazil
| | - Thaís Matos Ceacero
- APTA Center of Beef Cattle, Animal Science Institute, Sertaozinho, SP, Brazil
| | | | - Fernando Baldi
- School of Agricultural and Veterinarian Sciences, FCAV/ UNESP–Sao Paulo State University, Department of Animal Science, Jaboticabal-SP, Brazil
| | | | | | - Daniela Lino Lourenco
- University of Georgia, Department of Animal and Dairy Science, Athens, GA, United States of America
| | - Ignacy Misztal
- University of Georgia, Department of Animal and Dairy Science, Athens, GA, United States of America
| | - Lucia Galvão de Albuquerque
- School of Agricultural and Veterinarian Sciences, FCAV/ UNESP–Sao Paulo State University, Department of Animal Science, Jaboticabal-SP, Brazil
- * E-mail:
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27
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Urbinati I, Stafuzza NB, Oliveira MT, Chud TCS, Higa RH, Regitano LCDA, de Alencar MM, Buzanskas ME, Munari DP. Selection signatures in Canchim beef cattle. J Anim Sci Biotechnol 2016; 7:29. [PMID: 27158491 PMCID: PMC4858954 DOI: 10.1186/s40104-016-0089-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 04/24/2016] [Indexed: 11/10/2022] Open
Abstract
Background Recent technological advances in genomics have allowed the genotyping of cattle through single nucleotide polymorphism (SNP) panels. High-density SNP panels possess greater genome coverage and are useful for the identification of conserved regions of the genome due to selection, known as selection signatures (SS). The SS are detectable by different methods, such as the extended haplotype homozygosity (EHH); and the integrated haplotype score (iHS), which is derived from the EHH. The aim of this study was to identify SS regions in Canchim cattle (composite breed), genotyped with high-density SNP panel. Results A total of 687,655 SNP markers and 396 samples remained for SS analysis after the genotype quality control. The iHS statistic for each marker was transformed into piHS for better interpretation of the results. Chromosomes BTA5 and BTA14 showed piHS > 5, with 39 and nine statistically significant SNPs (P < 0.00001), respectively. For the candidate selection regions, iHS values were computed across the genome and averaged within non-overlapping windows of 500 Kb. We have identified genes that play an important role in metabolism, melanin biosynthesis (pigmentation), and embryonic and bone development. Conclusions The observation of SS indicates that the selection processes performed in Canchim, as well as in the founder breeds (i.e. Charolais), are maintaining specific genomic regions, particularly on BTA5 and BTA14. These selection signatures regions could be associated with Canchim characterization. Electronic supplementary material The online version of this article (doi:10.1186/s40104-016-0089-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ismael Urbinati
- Departamento de Ciências Exatas, - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo 14884-900 Brazil
| | - Nedenia Bonvino Stafuzza
- Departamento de Ciências Exatas, - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo 14884-900 Brazil
| | - Marcos Túlio Oliveira
- Departamento de Tecnologia, UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo 14884-900 Brazil
| | - Tatiane Cristina Seleguim Chud
- Departamento de Ciências Exatas, - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo 14884-900 Brazil
| | | | | | | | - Marcos Eli Buzanskas
- Departamento de Ciências Exatas, - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo 14884-900 Brazil
| | - Danísio Prado Munari
- Departamento de Ciências Exatas, - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo 14884-900 Brazil
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Stafuzza NB, Olivatto LM, Naressi BCM, Tonhati H, Amaral-Trusty MEJ. Analysis of DRB3 gene polymorphisms in Jafarabadi, Mediterranean, and Murrah buffaloes from Brazil. Genet Mol Res 2016; 15:gmr6368. [PMID: 27051015 DOI: 10.4238/gmr.15016368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The DRB3 gene is an MHC class II gene that has a high degree of polymorphism with more than 100 alleles described in cattle. This variation contributes to differences among individuals in immune responsiveness and disease resistance. In this study, we searched for allelic variants in exon 2 of the DRB3 gene in 80 river buffaloes of three breeds in Brazil using a PCR-RFLP technique. The PCR product showed genetic polymorphism when digested with RsaI, PstI or HaeIII restriction enzymes. In total, 16 restriction patterns were identified: nine restriction patterns and 16 genotypes were found with RsaI; four restriction patterns and nine genotypes were found with HaeIII; and, three restriction patterns and four genotypes were found with PstI. Three RFLP patterns were exclusive to Jafarabadi buffaloes (RsaI-b, RsaI-c and RsaI-f) and three others were only observed in Mediterranean buffaloes (RsaI-g, RsaI-h and PstI-y). Jafarabadi buffaloes had a larger number of RFLP patterns than Mediterranean and Murrah breeds. The analysis showed that the DRB3 exon 2 was highly polymorphic, with the highest degree of polymorphism in Mediterranean buffaloes. This study provides the first assessment of allelic variation among three different buffalo breeds from Brazil and provides a basis for further investigations into the association between the DRB3 alleles and disease resistance.
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Affiliation(s)
- N B Stafuzza
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho, São José do Rio Preto, SP, Brasil.,Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, SP, Brasil
| | - L M Olivatto
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho, São José do Rio Preto, SP, Brasil
| | - B C M Naressi
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho, São José do Rio Preto, SP, Brasil
| | - H Tonhati
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, SP, Brasil
| | - M E J Amaral-Trusty
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho, São José do Rio Preto, SP, Brasil
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Stafuzza NB, Naressi BCM, Borges MM, Amaral-Trusty MEJ. Sequence analysis of the S1PR1 gene in river buffalo. Genet Mol Res 2016; 15:gmr6363. [PMID: 26909928 DOI: 10.4238/gmr.15016363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Recent developments in methodologies for genomic analyses have enabled a significant advance in understanding of the river buffalo genome. The S1PR1 gene has been mapped to buffalo chromosome 6 and bovine chromosome 3; this gene is of interest as it is a candidate for marbling in meat, an important economic trait. Here, we performed next generation sequencing in a buffalo BAC DNA clone and obtained a 54.5-kb sequence encompassing the entire buffalo S1PR1 gene as well as the 27 kb upstream region and the 22 kb downstream region. The gene had a total length of 4716 bp, including three exons and two introns; exons 1 and 2 were classified as non-protein-coding. In comparison with homologues from other species, the structural organization of buffalo S1PR1 was closest to that of the goat and in both species exon 2 of the gene was non-protein-coding. One hundred and nine repetitive elements were found within the buffalo gene and its boundary regions, with 50 SINE repeats being the most abundant. Alignment of S1PR1 sequences from the Murrah and Mediterranean breeds revealed two nucleotide substitutions (g.1176C>G and g.2740T>C), which represent potential SNPs that could be used in further studies of buffalo genetic structure.
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Affiliation(s)
- N B Stafuzza
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho, São José do Rio Preto, SP, Brasil.,Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, SP, Brasil
| | - B C M Naressi
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho, São José do Rio Preto, SP, Brasil
| | - M M Borges
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho, São José do Rio Preto, SP, Brasil
| | - M E J Amaral-Trusty
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho, São José do Rio Preto, SP, Brasil
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Nogueira CA, Stafuzza NB, Ribeiro TP, Prado ADL, Menezes IPP, Peixoto N, Gonçalves PJ, Almeida LM. Intraspecific differentiation of Hancornia speciosa revealed by simple sequence repeat and random amplified polymorphic DNA markers. Genet Mol Res 2015; 14:15996-6005. [PMID: 26662392 DOI: 10.4238/2015.december.7.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Hancornia speciosa, popularly known as mangabeira, is a fruit tree native to the Brazilian Cerrado that shows great economic potential, due to its multiple uses. Intraspecific classification of this species is difficult because it shows high morphological diversity. An early study of the species reported that there are six botanic varieties that differ morphologically mainly in the shapes of their leaves and flowers. Except to note the wide morphological variation and economic potential of this species, few studies have been published about the genetic diversity of mangabeira. Knowledge of the genetic variability of this species among populations would be useful for genetic conservation and breeding programs. Therefore, we tested the transferability of 12 simple sequence repeats from expressed sequence tags (EST-SSRs) from Catharanthus roseus to H. speciosa and used 10 random amplified polymorphic DNA markers to evaluate the genetic variability among botanical varieties of H. speciosa. We obtained a high transferability frequency of EST-SSR markers from C. roseus to H. speciosa (75%). However, EST-SSR markers showed low heterozygosity and locus variability (two or three alleles by locus), which suggest low genetic diversity in the mangabeira samples. The Jaccard dissimilarity index and an examination of geographic distances indicated a non-spatial structuring of the genetic variability. Our markers were unable to distinguish H. speciosa botanical varieties.
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Affiliation(s)
- C A Nogueira
- Universidade Estadual de Goiás, Campus Anápolis de Ciências Exatas e Tecnológicas, Anápolis, GO, Brasil
| | - N B Stafuzza
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual de São Paulo "Júlio de Mesquita Filho", Jaboticabal, SP, Brasil
| | - T P Ribeiro
- Universidade Estadual de Goiás, Campus Ipameri, Ipameri, GO, Brasil
| | - A D L Prado
- Universidade Estadual de Goiás, Campus Ipameri, Ipameri, GO, Brasil
| | - I P P Menezes
- Laboratório de Genética e Biologia Molecular, Instituto Federal Goiano, Urutaí, GO, Brasil
| | - N Peixoto
- Universidade Estadual de Goiás, Campus Ipameri, Ipameri, GO, Brasil
| | - P J Gonçalves
- Instituto de Física, Universidade Federal de Goiás, Goiânia, GO, Brasil
| | - L M Almeida
- Universidade Estadual de Goiás, Campus Anápolis de Ciências Exatas e Tecnológicas, Anápolis, GO, Brasil
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31
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Stafuzza NB, Naressi BCM, Yang E, Cai JJ, Amaral-Trusty MEJ. A framework radiation hybrid map of buffalo chromosome 1 ordering scaffolds from buffalo genome sequence assembly. Genet Mol Res 2015; 14:13096-104. [PMID: 26535622 DOI: 10.4238/2015.october.26.5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
River buffalo chromosome 1 (BBU1) is a sub-metacentric chromosome homologous to bovine chromosomes 1 and 27. In this study, we constructed a new framework radiation hybrid (RH) map from BBU1 using BBURH5000 panel adding nine new genes (ADRB3, ATP2C1, COPB2, CRYGS, P2RY1, SLC5A3, SLC20A2, SST, and ZDHHC2) and one microsatellite (CSSM043) to the set of markers previously mapped on BBU1. The new framework RH map of BBU1 contained 141 markers (55 genes, 2 ESTs, 10 microsatellites, and 74 SNPs) distributed within one linkage group spanning 2832.62 centirays. Comparison of the RH map to sequences from bovine chromosomes 1 and 27 revealed an inversion close to the telomeric region. In addition, we ordered a set of 34 scaffolds from the buffalo genome assembly UMD_CASPUR_WB_2.0. The RH map could provide a valuable tool to order scaffolds from the buffalo genome sequence, contributing to its annotation.
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Affiliation(s)
- N B Stafuzza
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho, São José do Rio Preto, SP, Brasil
| | - B C M Naressi
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho, São José do Rio Preto, SP, Brasil
| | - E Yang
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - J J Cai
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - M E J Amaral-Trusty
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho, São José do Rio Preto, SP, Brasil
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32
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Venturini GC, Stafuzza NB, Cardoso DF, Baldi F, Ledur MC, Peixoto JO, El Faro L, Munari DP. Association between ACTA1 candidate gene and performance, organs and carcass traits in broilers. Poult Sci 2015; 94:2863-9. [PMID: 26476088 DOI: 10.3382/ps/pev285] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 08/10/2015] [Indexed: 11/20/2022] Open
Abstract
This study investigates the genetic association of the SNP present in the ACTA1 gene with performance traits, organs and carcass of broilers to help marker-assisted selection of a paternal broiler line (TT) from EMBRAPA Swine and Poultry, Brazil. Genetic and phenotypic data of 1,400 broilers for 68 traits related to body performance, organ weights, weight of carcass parts, and yields as a percentage of organs and carcass parts were used. The maximum likelihood method, considering 4 analytical models, was used to analyze the genetic association between the SNP and these important economic traits. The association analysis was performed using a mixed animal model including the random effect of the animal (polygenic), and the fixed effects of sex (2 levels), hatch (5 levels) and SNP (3 levels), besides the random error. The traits significantly associated (P<0.05) with the SNP were analyzed, along with body weight at 42 days of age (BW42), by the restricted maximum likelihood method using the multi-trait animal model to estimate genetic parameters. The analysis included the residual and additive genetic random effects and the sex-hatch fixed effect. The additive effects of the SNP were associated with breast meat (BMY), liver yield (LIVY), body weight at 35 days of age (BW35); drumstick skin (DSW), drumstick (DW) and breast (BW) weights. The heritability estimates for these traits, in addition to BW42, ranged from 0.24±0.06 to 0.45±0.08 for LIVY and BW35, respectively. The genetic correlation ranged from 0.02±0.18 for LIVY and BMY to 0.97±0.01 for BW35 and BW42. Based on the results of this study, it can be concluded that ACTA1 gene is associated with performance traits BW35, LIV and BMY, DW, BW and DW adjusted for body weight at 42 days of age. Therefore, the ACTA1 gene is an important molecular marker that could be used together with others already described to increase the economically important traits in broilers.
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Affiliation(s)
- G C Venturini
- UNESP São Paulo State University, College of Agriculture and Veterinary Sciences, 14884-900, Jaboticabal (SP), Brazil
| | - N B Stafuzza
- UNESP São Paulo State University, College of Agriculture and Veterinary Sciences, 14884-900, Jaboticabal (SP), Brazil
| | - D F Cardoso
- UNESP São Paulo State University, College of Agriculture and Veterinary Sciences, 14884-900, Jaboticabal (SP), Brazil
| | - F Baldi
- UNESP São Paulo State University, College of Agriculture and Veterinary Sciences, 14884-900, Jaboticabal (SP), Brazil
| | - M C Ledur
- Embrapa Suínos e Aves, 89700-000, Concórdia (SC), Brazil
| | - J O Peixoto
- Embrapa Suínos e Aves, 89700-000, Concórdia (SC), Brazil
| | - L El Faro
- Agencia Paulista de Tecnologia dos Agronegócios (APTA) Centro Leste/Secretaria de Agricultura e Abastecimento (SAA), 14001-970, Ribeirão Preto (SP), Brazil
| | - D P Munari
- UNESP São Paulo State University, College of Agriculture and Veterinary Sciences, 14884-900, Jaboticabal (SP), Brazil
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Stafuzza NB, Borges MM, Amaral-Trusty MEJ. Molecular characterization of interferon regulatory factor 1 in Bubalus bubalis. Genet Mol Res 2015; 14:10919-28. [PMID: 26400319 DOI: 10.4238/2015.september.21.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Interferon regulatory factor 1 (IRF1) is functionally diverse in the regulation of immune response and is considered to be an important candidate gene for studying disease susceptibility in mammals. In this paper, we characterized the whole sequence of the IRF1 gene in river buffalo (Bubalus bubalis) and compared genomic and the amino acid sequences between different species. The buffalo IRF1 gene was 7099 bp long and organized into 10 exons and nine introns. Its molecular structure showed exactly the same number of exons (10) and introns (nine) in bovids, mice, horses, humans, and chickens. However, rats did not have exon 5, but had the largest exon 4, which suggests that exon 5 was incorporated into exon 4. The coding and the amino acid sequences of the gene showed that identity varied from 73 to 99% at the coding sequence level and from 61 to 100% at the amino acid level when compared with other mammals and chickens. Comparative analysis of the gene sequence between two different buffalo breeds, Murrah and Mediterranean, revealed six potential SNPs that are primarily located in the 5' and 3'UTRs.
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Affiliation(s)
- N B Stafuzza
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto, SP, Brasil
| | - M M Borges
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto, SP, Brasil
| | - M E J Amaral-Trusty
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto, SP, Brasil
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da Cruz VAR, Schenkel FS, Savegnago RP, Grupioni NV, Stafuzza NB, Sargolzaei M, Ibelli AMG, Peixoto JDO, Ledur MC, Munari DP. Association of Apolipoprotein B and Adiponectin Receptor 1 Genes with Carcass, Bone Integrity and Performance Traits in a Paternal Broiler Line. PLoS One 2015; 10:e0136824. [PMID: 26322976 PMCID: PMC4555837 DOI: 10.1371/journal.pone.0136824] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 08/09/2015] [Indexed: 11/25/2022] Open
Abstract
Apolipoprotein B (APOB) and Adiponectin Receptor 1 (ADIPOR1) are related to the regulation of feed intake, fat metabolism and protein deposition and are candidate genes for genomic studies in birds. In this study, associations of two single nucleotide polymorphisms (SNPs) g.102A>T (APOB) and g.729C>T (ADIPOR1) with carcass, bone integrity and performance traits in broilers were investigated. Genotyping was performed on a paternal line of 1,454 broilers. The SNP detection was carried out by PCR-RFLP technique using the restriction enzymes HhaI for the SNP g.729C>T and MslI for the SNP g.102A>T. The association analyses of the two SNPs with 85 traits were performed using the restricted maximum likelihood (REML) and Generalized Quasi-Likelihood Score (GQLS) methods. For REML the model included the random additive genetic effect of animal and fixed effects of sex, hatch and SNP genotypes. In the GQLS method, a logistic regression was used to associate the genotypes with phenotypes adjusted for fixed effects of sex and hatch. The SNP g.729C>T in the ADIPOR1 gene was associated with thickness of the femur and breast skin yield. Thus, the ADIPOR1 gene seems implicated in the metabolism and/or fat deposition and bone integrity in broilers.
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Affiliation(s)
- Valdecy Aparecida Rocha da Cruz
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias (FCAV),Universidade Estadual Paulista (UNESP), Jaboticabal, São Paulo, Brasil
| | | | - Rodrigo Pelicioni Savegnago
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias (FCAV),Universidade Estadual Paulista (UNESP), Jaboticabal, São Paulo, Brasil
| | - Natalia Vinhal Grupioni
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias (FCAV),Universidade Estadual Paulista (UNESP), Jaboticabal, São Paulo, Brasil
| | - Nedenia Bonvino Stafuzza
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias (FCAV),Universidade Estadual Paulista (UNESP), Jaboticabal, São Paulo, Brasil
| | | | | | | | | | - Danísio Prado Munari
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias (FCAV),Universidade Estadual Paulista (UNESP), Jaboticabal, São Paulo, Brasil
- * E-mail:
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Stafuzza NB, Borges MM, Amaral-Trusty MEJ. Sequence characterization and comparative analysis of the gastrotropin gene in buffalo (Bubalus bubalis). Genet Mol Res 2014; 13:10934-42. [PMID: 25526214 DOI: 10.4238/2014.december.19.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In this study, we compared the complete sequence of the FABP6 gene from an animal representing the Murrah breed of the river buffalo (Bubalus bubalis) with the gene sequence from different mammals. The buffalo FABP6 gene is 6105 bp in length and is organized into four exons (67, 176, 90, and 54 bp), three introns (1167, 1737, and 2649 bp), a 5ꞌUTR (93 bp), and a 3ꞌUTR (72 bp). A total of 22 repetitive elements were identified at the intronic level, and four of these (L1MC, L1M5, MIRb, and Charlie4z) were identified as being exclusive to buffalo. Comparative analysis between the FABP6 gene coding sequence and the amino acid sequence with its homologues from other mammalian species showed a percentage of identity varying from 79 to 98% at the DNA coding level and 70 to 96% at the amino acid level. In addition, the alignment of the gene sequence between the Murrah and the Mediterranean breeds revealed 20 potential single nucleotide polymorphisms, which could be candidates for validation in commercial buffalo populations.
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Affiliation(s)
- N B Stafuzza
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista São José do Rio Preto, SP, Brasil
| | - M M Borges
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista São José do Rio Preto, SP, Brasil
| | - M E J Amaral-Trusty
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista São José do Rio Preto, SP, Brasil
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Venturini GC, Cardoso DF, Baldi F, Freitas AC, Aspilcueta-Borquis RR, Santos DJA, Camargo GMF, Stafuzza NB, Albuquerque LG, Tonhati H. Association between single-nucleotide polymorphisms and milk production traits in buffalo. Genet Mol Res 2014; 13:10256-68. [PMID: 25501237 DOI: 10.4238/2014.december.4.20] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The aim of this study was to identify single-nucleotide polymorphisms (SNPs) in buffaloes associated with milk yield and content, in addition to somatic cell scores based on the cross-species transferability of SNPs from cattle to buffalo. A total of 15,745 SNPs were analyzed, of which 1562 showed 1% significance and 4742 with 5% significance, which were associated for all traits studied. After application of Bonferroni's correction for multiple tests of the traits analyzed, we found 2 significant SNPs placed on cattle chromosomes BTA15 and BTA20, which are homologous to buffalo chromosomes BBU16 and BBU19, respectively. In this genome association study, we found several significant SNPs affecting buffalo milk production and quality. Furthermore, the use of the high-density bovine BeadChip was suitable for genomic analysis in buffaloes. Although extensive chromosome arm homology was described between cattle and buffalo, the exact chromosomal position of SNP markers associated with these economically important traits in buffalo can be determined only through buffalo genome sequencing.
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Affiliation(s)
- G C Venturini
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
| | - D F Cardoso
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
| | - F Baldi
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
| | - A C Freitas
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
| | - R R Aspilcueta-Borquis
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
| | - D J A Santos
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
| | - G M F Camargo
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
| | - N B Stafuzza
- Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto, SP, Brasil
| | - L G Albuquerque
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
| | - H Tonhati
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
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37
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Stafuzza NB, Borges MM, Amaral MEJ. Comparative analysis of the river buffalo somatostatin gene. Genet Mol Res 2014; 13:10017-24. [PMID: 25501213 DOI: 10.4238/2014.november.28.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The somatostatin protein plays a crucial role in the regulation of multiple biological functions, such as growth, fat deposition, and nutrient absorption in vertebrates. Polymorphisms in the somatostatin gene have been associated with growth traits in livestock species, including cattle and goat. In this study, we conducted complete molecular characterization of the somatostatin gene in Bubalus bubalis (Murrah breed) by sequencing a Murrah BAC clone spanning 72,489 base pairs (bp) in length. The buffalo somatostatin gene contains 1481 bp organized into a 5'-untranslated region (135 bp), exon 1 (139 bp), intron 1 (839 bp), exon 2 (212 bp), and 3'UTR (156 bp). Comparative analysis between the buffalo somatostatin DNA coding sequence and the amino acid sequence with other bovids (cattle, goat, and sheep), horse, pig, human, rodents (mouse and rat), and chicken. Identity varied from 83-99% on the DNA sequence level and 88-100% on the protein level. In addition, a comparison of gene sequences between Murrah and Mediterranean breeds revealed 6 potential single-nucleotide polymorphisms (1 in exon 1 and 5 in intron 1), which were validated in different buffalo populations. This comparative analysis provides basic information for future studies of different buffalo herds using the position candidate gene approach, quantitative trait loci analysis, and polymorphisms associated with growth traits.
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Affiliation(s)
- N B Stafuzza
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto, SP, Brasil
| | - M M Borges
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto, SP, Brasil
| | - M E J Amaral
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto, SP, Brasil
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38
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Stafuzza NB, Greco AJ, Grant JR, Abbey CA, Gill CA, Raudsepp T, Skow LC, Womack JE, Riggs PK, Amaral MEJ. A high-resolution radiation hybrid map of the river buffalo major histocompatibility complex and comparison with BoLA. Anim Genet 2012; 44:369-76. [PMID: 23216319 DOI: 10.1111/age.12015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2012] [Indexed: 02/03/2023]
Abstract
The major histocompatibility complex (MHC) in mammals codes for antigen-presenting proteins. For this reason, the MHC is of great importance for immune function and animal health. Previous studies revealed this gene-dense and polymorphic region in river buffalo to be on the short arm of chromosome 2, which is homologous to cattle chromosome 23. Using cattle-derived STS markers and a river buffalo radiation hybrid (RH) panel (BBURH5000 ), we generated a high-resolution RH map of the river buffalo MHC region. The buffalo MHC RH map (cR5000 ) was aligned with the cattle MHC RH map (cR12000 ) to compare gene order. The buffalo MHC had similar organization to the cattle MHC, with class II genes distributed in two segments, class IIa and class IIb. Class IIa was closely associated with the class I and class III regions, and class IIb was a separate cluster. A total of 53 markers were distributed into two linkage groups based on a two-point LOD score threshold of ≥8. The first linkage group included 32 markers from class IIa, class I and class III. The second linkage group included 21 markers from class IIb. Bacterial artificial chromosome clones for seven loci were mapped by fluorescence in situ hybridization on metaphase chromosomes using single- and double-color hybridizations. The order of cytogenetically mapped markers in the region corroborated the physical order of markers obtained from the RH map and served as anchor points to align and orient the linkage groups.
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Affiliation(s)
- N B Stafuzza
- Department of Biology, UNESP - São Paulo State University, IBILCE, Sao Jose do Rio Preto, SP, 15054-000, Brazil
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39
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Stafuzza NB, Abbey CA, Gill CA, Womack JE, Amaral MEJ. Construction and preliminary characterization of a river buffalo bacterial artificial chromosome library. Genet Mol Res 2012; 11:3013-9. [PMID: 22653673 DOI: 10.4238/2012.may.22.6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
River buffalo genome analyses have advanced significantly in the last decade, and the genome sequence of Bubalus bubalis will be available shortly. Nonetheless, large-insert DNA library resources such as bacterial artificial chromosomes (BAC) are still required for validation and accurate assembly of the genome sequence. We constructed a river buffalo BAC library containing 52,224 clones with an average insert size of 97 kb, representing 1.7 × coverage of the genome. This genomic resource for river buffalo will facilitate further studies in this economically important species allowing for instance, whole genome physical mapping and isolation of genes and gene clusters, contributing to the elucidation of gene organization and identification of regulatory elements.
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Affiliation(s)
- N B Stafuzza
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual de São Paulo "Júlio de Mesquita Filho", São José do Rio Preto, SP, Brazil
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40
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Stafuzza NB, Abbassi H, Grant JR, Rodrigues-Filho EA, Ianella P, Kadri SM, Amarante MV, Stohard P, Womack JE, de León FAP, Amaral MEJ. Comparative RH maps of the river buffalo and bovine Y chromosomes. Cytogenet Genome Res 2009; 126:132-8. [PMID: 20016162 DOI: 10.1159/000245912] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2009] [Indexed: 11/19/2022] Open
Abstract
Radiation hybrid maps were constructed for river buffalo and cattle Y chromosomes. A total of 41 cattle-derived Y-chromosome molecular markers were selected and tested with 2 previously described 5,000-rad whole-genome radiation hybrid (RH) panels (river buffalo - BBURH(5000) and cattle - BTARH(5000)) for generation of maps. Among the initial 41 selected markers, a subset of 26 markers generated PCR products suitable for scoring with the BBURH(5000) panel. Of these, 19 markers (73%) were distributed in 1 linkage group spanning 341.3 cR. Retention frequencies (RF) for individual markers ranged from 17.8% for SMCY to 56.7% for BTY1, with an average RF of 37.6%. From the selected markers, 37 generated reliable scores using the BTARH(5000) panel. The newly constructed BTAY RH map contains 28 markers distributed within 1 linkage group. Twenty-four of these markers had been previously mapped on BTAY using a 7,000-rad cattle-hamster WG-RH panel and 4 markers were mapped for the first time (ZFY, SeqRep, RepSeqS4 and BTY1). The length of the BTAY RH map was estimated to be 602.4 cR. Retention frequencies for individual mapped markers ranged from 10% (INRA126) to 63.3% (SeqRep), with an average RF of 35.3%. RH marker positions along the Y chromosome were compared between BBUY and BTAY, which revealed differences in the order of some of the markers. The BBUY pseudoautosomal region (PAR) is delineated by 3 BTAY PAR markers (MAF45, TGLA325 and UMN2008). These markers are telomeric in both species but are not found in the same order. Here we have demonstrated the effective use of bovine Y chromosome markers for the development of the first BBUY RH map. Likewise, these set of markers can be used for comparative assessment of Y chromosomes in other members of the Bovidae family.
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Affiliation(s)
- N B Stafuzza
- UNESP - São Paulo State University, IBILCE, Dept. Biologia, São José Rio Preto, SP, Brazil
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41
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Stafuzza NB, Kata S, Womack JE, Amaral MEJ. Mapping the BDA20 gene to BTAX. ACTA ACUST UNITED AC 2008; 132:359-361. [PMID: 18817327 DOI: 10.1159/000317186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The lipocalin family is a large group of proteins that exhibits great structural and functional variation both within and among species, including a significant number of animal-derived aeroallergens, such as the bovine BDA20 (major cow dander allergen). This protein is classified as an occupational allergen causing asthma and other work-related allergic disorders among dairy farmers. Using a somatic cell panel the BDA20 gene was assigned to the bovine X chromosome (BTAX) with a significant concordant value of 97% to the previously mapped reference marker MAF45. A radiation hybrid (RH) mapping approach confirmed the assignment of BDA20 to BTAX. Two-point LOD scores showed that BDA20 is linked to XBM451 with a LOD score of 22.1 for a theta value of 0.03.
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Ianella P, Venancio LPR, Stafuzza NB, Miziara MN, Agarwala R, Schäffer AA, Riggs PK, Womack JE, Amaral MEJ. First radiation hybrid map of the river buffalo X chromosome (BBUX) and comparison with BTAX. Anim Genet 2008; 39:196-200. [PMID: 18307583 DOI: 10.1111/j.1365-2052.2007.01696.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the first radiation hybrid map of the river buffalo X chromosome generated from a recently constructed river buffalo (Bubalus bubalis) whole-genome radiation hybrid panel (BBURH(5000)). This map contains a total of 33 cattle-derived markers, including 10 genes, four ESTs and 19 microsatellites. The markers are distributed in two linkage groups: LG1 contains eight markers spanning 125.6 cR, and LG2 contains 25 markers spanning 366.3 cR. LG1 contains six markers in common with bovine sequence assembly build 3.1. With the exception of BMS2152, the order of these markers on our BBUX map is shuffled when compared to the cow X chromosome (Bos taurus; BTAX). From LG2, two markers (AMELX and BL22) map to a more distal portion of BTAX compared to BBUX. In addition, two pairs of LG2 markers exhibit inversions compared to BTAX (ILSTS017 and ATRX; XBM38 and PPEF1). Alternatively, when compared to the most recent bovine RH map (Bov-Gen 3000rads), BL1098 and BMS2227 from LG1 as well as PLS3 and BMS1820 from LG2 showed inverted positions on the BBUX map. These discrepancies in buffalo and cattle maps may reflect evolutionary divergence of the chromosomes or mapping errors in one of the two species. Although the set of mapped markers does not cover the entire X chromosome, this map is a starting point for the construction of a high-resolution map, which is necessary for characterization of small rearrangements that might have occurred between the Bubalus bubalis and Bos taurus X chromosomes.
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Affiliation(s)
- P Ianella
- Dept. Biologia, IBILCE, UNESP - São Paulo State University, São Jose Rio Preto, SP 15054-000, Brazil
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Miziara MN, Goldammer T, Stafuzza NB, Ianella P, Agarwala R, Schaffer AA, Elliott JS, Riggs PK, Womack JE, Amaral MEJ. A radiation hybrid map of river buffalo (Bubalus bubalis) chromosome 1 (BBU1). Cytogenet Genome Res 2007; 119:100-4. [PMID: 18160788 DOI: 10.1159/000109625] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2007] [Accepted: 04/27/2007] [Indexed: 11/19/2022] Open
Abstract
The largest chromosome in the river buffalo karyotype, BBU1, is a submetacentric chromosome with reported homology between BBU1q and bovine chromosome 1 and between BBU1p and BTA27. We present the first radiation hybrid map of this chromosome containing 69 cattle derived markers including 48 coding genes, 17 microsatellites and four ESTs distributed in two linkage groups spanning a total length of 1330.1 cR(5000). The RH map was constructed based on analysis of a recently developed river buffalo-hamster whole genome radiation hybrid (BBURH(5000)) panel. The retention frequency of individual markers across the panel ranged from 17.8 to 52.2%. With few exceptions, the order of markers within linkage groups is identical to the order established for corresponding cattle RH maps. The BBU1 map provides a starting point for comparison of gene order rearrangements between river buffalo chromosome 1 and its bovine homologs.
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Affiliation(s)
- M N Miziara
- Departamento Biologia, UNESP - São Paulo State University, IBILCE, São Jose Rio Preto, Brazil
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44
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Stafuzza NB, Ianella P, Miziara MN, Agarwala R, Schäffer AA, Riggs PK, Womack JE, Amaral MEJ. Preliminary radiation hybrid map for river buffalo chromosome 6 and comparison to bovine chromosome 3. Anim Genet 2007; 38:406-9. [PMID: 17559550 DOI: 10.1111/j.1365-2052.2007.01612.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present the first radiation hybrid (RH) map of river buffalo (Bubalus bubalis) chromosome 6 (BBU6) developed with a recently constructed river buffalo whole-genome RH panel (BBURH(5000)). The preliminary map contains 33 cattle-derived markers, including 12 microsatellites, 19 coding genes and two ESTs, distributed across two linkage groups. Retention frequencies for markers ranged from 14.4% to 40.0%. Most of the marker orders within the linkage groups on BBU6 were consistent with the cattle genome sequence and RH maps. This preliminary RH map is the starting point for comparing gene order between river buffalo and cattle, presenting an opportunity for the examination of micro-rearrangements of these chromosomes. Also, resources for positional candidate cloning in river buffalo are enhanced.
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Affiliation(s)
- N B Stafuzza
- Department of Biologia, UNESP - São Paulo State University, IBILCE, São Jose Rio Preto, SP 15054-000, Brazil
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